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r1108: fixed missing inversions for #816 and #806

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Heng Li
2021-10-04 16:34:30 -04:00
parent aefa2c0d86
commit 39bdd45875
5 changed files with 27 additions and 8 deletions
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hit.c
+17 -1
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@@ -252,7 +252,7 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
mm_set_sam_pri(n_regs, regs);
}
void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r)
void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int check_strand, int min_strand_sc, int *n_, mm_reg1_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_, n_2nd = 0;
@@ -264,6 +264,9 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_,
if (!(r[i].qs == r[p].qs && r[i].qe == r[p].qe && r[i].rid == r[p].rid && r[i].rs == r[p].rs && r[i].re == r[p].re)) // not identical hits
r[k++] = r[i], ++n_2nd;
else if (r[i].p) free(r[i].p);
} else if (check_strand && n_2nd < best_n && r[i].score > min_strand_sc && r[i].rev != r[p].rev) {
r[i].strand_retained = 1;
r[k++] = r[i], ++n_2nd;
} else if (r[i].p) free(r[i].p);
}
if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
@@ -271,6 +274,19 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_,
}
}
int mm_filter_strand_retained(int n_regs, mm_reg1_t *r)
{
int i, k;
for (i = k = 0; i < n_regs; ++i) {
int p = r[i].parent;
if (!r[i].strand_retained || r[i].div < r[p].div * 5.0f) {
if (k < i) r[k++] = r[i];
else ++k;
}
}
return k;
}
void mm_filter_regs(const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs)
{ // NB: after this call, mm_reg1_t::parent can be -1 if its parent filtered out
int i, k;